The Imperial-Covenant War
by Kobertron
Summary: What if the Covenant didn't try to kill humanity? What if they integrated them instead? What if the Empire expanded past the borders with the dawn of their superweapon? What if these two powerful empires clashed? The result, a war larger than most in the galaxy could even imagine.
1. Chapter 1

**Oi! I am new to fanfiction and this idea popped in my head while playing Halo Reach a wee past my bedtime. I made a timeline to make sense of things before I bother starting any actual writing so I can see if people want this made or not. I might change things if it needs to be changed. Still indecisive on certain ideas I have.**

2524- The Covenant discover humanity. The High Prophets call for caution after discovering the rich abundance of Forerunner relics in the systems the human's dwelled in.

February, 2525- Contact between a civilian freighter and a Covenant vessel occurs over the colony of Harvest. More Covenant ships arrive, the commanding Elites ordering the others to not engage.

February 10th, 2525- A UNSC battlegroup is dispatched to Harvest, fearing the threat of a insurrection attack. Only to instead find the Covenant peacefully helping Harvest develop into a Covenant agriculture world.

February 11th, 2525- The Covenant commander of the fleet sends his full report to the hierarchs. Meetings are called by the Prophets.

February 17th, 2525- The Council votes to send multiple fleets to human colonies as a show of might. UNSC battle groups are called to the colonies in response, but neither side engages.

February 18th, 2525- A human-Sangheili research coalition enter the Forerunner temple on Harvest. After deep searching, the map room is discovered. All are surprised at how the Forerunner technology responds to human interaction.

February 20th, 2525- Fearing their power would be gone if the truth were to spread, the Prophets order all Brute forces to attack the humans and Elites. Several human ships are lost, as well as two Elite ships before they overpowered the inferior Brute soldiers.

February 28th, 2525- The UNSC declare war on the alien attackers. The need for the Spartan II's seemed more vital than ever, and are ready to be deployed.

March 1st, 2525- After the truth of the Halo array is revealed, Elite led Covenant forces execute the High Prophets Truth, Regret, and Mercy aboard High Charity. The furious Covenant species vow to exterminate any that supported the deceiving Prophets.

March 3rd, 2525- With the Covenant hierarchy changed, the Elites offer humanity a place in the Covenant.

March 8, 2525- Fearing resticance would only bring annihilation, UEG leaders agree to Covenant terms. Humanity officially joins the Covenant Empire after the death of the High Prophets. The Brutes are placed on the same level as grunts, with humanity quickly climbing the ladder in the caste system.

March 12, 2525- A treaty is signed on the battle scarred ground of Harvest. Admiral Terrence Hood and Thel 'Vadamee, both high Naval leaders, sign a pact of technological innovation and study, a mostly one sided promise to integrate warfare technology from each other's own equipment. Human AI prove to be the only thing of use the Covenant know the humans possess. Human ships now possess shielding and superior slipspace abilities while still using their traditional projectile based weapons.

April, 2525- Spartan-II's are integrated with Covenant shielding and cloak technology.

July, 2525- Covenant assist in the development of existing colonies.

December, 2525- A rebellion of human insurrectionists and Kig-yar pirates begins to rise. The rebellion tries to gain a footing by capturing Vice Admiral Preston Cole and numerous wealthy politicians. Spartan Blue team is tasked to rescue the hostages aboard a Kig-yar pirate ship, and manage to do so with no casualties, impressing many Elite warriors and adding new respect to humans.

February, 2526- The rebellion is officially crushed at the planet Mamore. The threat of more rebellion causes increase in security. Elite and grunt squads are officially assigned to every human vessel and world.

May, 2526- The UNSC designs and manufactures new plasma resistant armor and jumpsuits for Marines, allowing them to possess and be around Covenant based weapons without fear of severe plasma radiation damage to the body.

 **Thanks for reading, hope you enjoyed.** Yes **I know it is short. Please leave a review discussing your deep emotional feelings that I'm totally sure you got from this exciting introduction. ;)**


	2. Section 1: Chapter 1

**Thanks for the awesome feedback guys and gals! I'm really happy you all mostly enjoyed the timeline and the ideas in it. I made this as soon as possible. Although I had some trouble lengthening everything to make it an appropriate size, whatever, I'm sure you're not even reading this, and why would you? Get your butt to the story you dingus!**

 **Section I: Aggressive Expansion**

 **Chapter 1**

 **July 3, 2532 (UEG Calendar)**

 **Reach, Epsilon Eridani System**

 **Bighorn River Base**

Private Steven Hernandez collapsed to the mud covered ground with a grunt. Training rounds barely grazing over his helmet. The turret fired a constant barrage of rubber rounds, carrying enough force to knock a regular human on his rear.

Gal 'Monrara lifted the the twenty nine year old marine to his feet, and back to his cover behind the prop of a damaged wraith.

"That was reckless Hernandez!" Sergeant Avery Johnson barked. "Stupid shit that like will get you killed in live combat!"

"Sorry Sarge, I just thought I could-" Steven tried to apologize while looking at his dirty SPI armor, rubbing mud off the shield generator pack on his backside.

"Can it marine! Wait for the order, got it?" Steven nodded in response, gulping his saliva as he wiped off the mud on his face.

Gal glared at the frustrated Sergeant, then looked back to the AI controlled turret in the bunker. Lius 'Kalami lifted his plasma rifle, gesturing the rest of the squad to move on them as the turret continued its barrage.

The war simulation started as a disaster, enemy marksmen and turrets managed to disable most of the platoon, all the grunts were downed after falling into an ambush, nearly a dozen grunts were now out of the 'game', all for just one of the three flags. It was captured of course, as well as another placed in a tower. All that remained was the final flag in the bunker. Out of the thirty six troops, only seven remained. Dagger platoon used to have a record of efficient wins, now they might as well be recruit level with the losses amounted in a simple capture the flag simulation.

The Elite and human joined their comrades, one less than what Johnson previously known remained of his platoon. The Elite fired off rounds to cover his and the marine's advance, more muscle memory than anything, there was no point in shooting at somewhere that no real enemy resides. Nothing to frighten with plasma bolts. The human rolled by the end, creeping her head over the cover to get a better look. The Elite also crouched near the end of his cover, examining the battlefield for a weakness. Little cover, just a straight line to the small bunker.

"Where's Taco?" Johnson asked the two soldiers.

Gal snorted at the humans mispronunciation of the missing Sangheili's name, then gestured to the said Elite. "Blademaster Teko seems to be sneaking away from his previous cover."

"Comrades!" Teko 'Kadam's voice shouted gleefully through the comm. "I will distract our adversary, advance and capture your objective!"

"What is he doing?" Private Tamera shook her head as the young blademaster began to charge, firing his plasma rifle in defiance of the turret.

"There!" An enemy marine shouted. "Fire on that Elite!"

Two marines armed with training assault rifles fired several bursts at the swordsman. His shields shrugged off the training rounds and he continued his charge to the enemy.

"Well," Steven shrugged as Teko roared a battle cry, "I guess we better get moving."

Gal nodded, leading the charge against the distracted turret. The turret switched targets faster than anticipated, firing into Gal and Tamera, essentially knocking them out of the game.

Steven and Johnson took the opportunity, diving past their downed teammates and around the turret's line of site. No one else managed to get inside, but the two could still hear Teko's roars, he was obviously enjoying himself too much. Teko was naturally acrobatic, proving his skill enough to become a blade master despite his young age.

Teko rolled away, ducking and jumping as much as he could while Johnson and Steven made their way inside.

Rubber bullets ricocheted off Teko's armor and he barely kept himself up.

Johnson sighed, catching his breath before disabling the turret, Steven grabbing the purple-gold flag, ending the simulation.

The platoon reassembled, eighteen grunts, six elites, and twelve marines all walked back to their 'spawn base'. A hologram of their score lit up as they walked outside the simulation zone, their platoon title went from second to fourth place, they didn't score well.

A phantom flew overhead with its complementary escort of two banshees, changing course to avoid the large energy spire that stood above all else in the entire region.

Squads jogged around the perimeter of the mess hall, saluting at the passing scout warthog, it's passenger being one of the most important military officials on the planet, the Master Brigadier.

The thirty six soldiers of three different races all lined up and formed into three long rows, each standing to attention while in face of the Master Brigadier, Jonathan Price.

"Dagger platoon has failed the time limit portion of the simulation, by several minutes. Rome and Noble platoons finished their simulations in half the time of your score. Do any of you understand why this troubles me?"

No one answered until he asked for the Sergeant. Johnson quickly spoke up, "You worry about planetary security, sir!"

"Yes." He nodded, pacing down the line of troops. "Every soldier in our military serves purpose, each are the bricks in our wall of defense, but if one of the bricks is loose or not strong enough, it can cause severe damage if an enemy finds that weak brick in the wall." He paused for a second to emphasize his analogy. "Need I remind you all that the URF and Prophet Loyalists still roam the stars? Terrorism and rebellion is not tolerated in our Covenant. We must always show our superior strength, and never stop preparing for attacks."

Everyone saluted, most wanting to leave from the lecture.

"Yeah, like they're ever gonna attack Reach." Steven muttered silently, knowing best to keep his thoughts to himself and not to the Master Brigadier. He did not want toilet duty again.

Reach was a military focal point in the Covenant Empire, a major human military world right on the doorstep of Earth, the human homeworld. Reach was one of the most essential planets in the Covenant Empire, with millions of soldiers training for any conflict and with dozens of bases researching forerunner technology to upgrade just about everything in the Empire. Human engineers and tech specialists would constantly study the forerunner relics on the planet, using what they learned to advance engines, shielding, and energy output in their starships.

Saying it was well defended would be putting it lightly, with a massive defense fleet protecting it, consisting of not to mention the twenty orbital defense stations placed around the vital world. Hundreds of capital ships and frigates guarded the planet and the system around it, making it one of the most well defended systems in the Covenant Empire.

Everyone in the Covenant knew that attacking the planet would be suicide. The best fighters, the best ships, and the best commanders in the sector were all stationed at Reach. With it's soldiers training to be the best.

"Good, now get some rest, you will try again at 0500 tomorrow." He finished before his warthog drove off.

 **Covenant World, Second Spark**

 **Edge of Unggoy Ricefields**

Jerap was about to fall asleep again. He and his fellow Unggoy, more commonly known in the Covenant as grunts, had been working with little breaks for several hours farming in massive fields of rice. _Second Spark_ was a small agriculture world, its main produce was cash crops like rice, Irukan, and wheat.

Second _Spark_ was only protected by a small fleet, a single carrier and a mere three cruisers, nothing serious to protect a small world. But it did had numerous transports and large human freighters delivering goods from the world to other colonies in the sector.

A single battalion of Jackals and Elites were detached on the farmlands, providing security against thieves and wildlife, and to keep everything in check. Single Jackals and Elites were positioned over every half mile of the rice fields.

Jerap scratched the top of his head, looking around to see the nearest Kig-yar sentry. Jackals were often placed to watch over grunt workers to keep them from wandering off or falling asleep.

The Jackal's back was turned, not looking in Jerap's direction. Good. His eyes blinked slowly, leaning on his rake, he slowly drifted to sleep.

The crash snapped Jerap awake, his fellow Unggoy were all chattering about the sudden object that fell from the sky.

Jerap turned his head, curious as to what had landed so close. The Jackal pulled his carbine, and slowly walked from his small encampment and towards the site of the crash. Several curious grunts followed behind, Jerap slowly did the same.

The site was just barely behind a set of rocks, smoke calmly rose, but there was little debris to be found.

Suddenly, a red flash of energy fired into the side of the Jackal, wounding the creature and causing him to shriek in pain. Many grunts yelled in fear, which grew as a black robot of unknown origin slowly floated into the clearing, firing it's weapon at the confused grunts.

Jerap also ran, for cover. His fellow grunts were not warriors, they were but farmers, not at all prepared for any attack.

Jerap looked around, spotting the now dead Jackal and his two guns, the carbine, and the plasma pistol holstered on his side. Jerap knew how the pistol functioned, and decided to use what little knowledge he had.

Jerap dove for the Jackal's body, allowing the others to be a distraction. He quickly reached for the plasma pistol from the magnetic holster, almost dropping the weapon while he fiddled with it.

The Imperial probe droid turned its head, and fired towards Jerap, barely missing the methane tank on his back as he ran back behind an old tree stump.

This was his chance to prove that he was more than just some worker. He ran out from behind the stump, and fired the charged bolt of plasma into the floating robot, shutting down it's systems and completely disabling it. But not before it was able to transmit what it was designed to find.

 **Sangheili Colony, Rahnelo**

 **Southern Hemisphere**

 **Keep of Clan 'Zahran**

The two massive doors of illuminating purple and gold opened silently, as the large Sangheili Kaidon, a high ranking Sangheili of the world, slowly wandered into the courtyard. His feet rubbed onto the soft grass, relieving the itch under his foot.

Vien 'Zahran looked to the night sky with a sigh, his cool robe fluttering by a sudden, yet calm, gust of wind. Breathing slowly through his nostrils, he felt relaxed. The moon illuminated the night sky like plasma in a dark hallway.

The porch was barely lit by large, ceremonial candles that made their way from the keep to the edge of the cliff.

Everything was peaceful, exactly what the old Sangheili was in the mood for after yet another restless sleep.

That was, until an unarmed Spectre drove through the dark forest, it's pink armor contrasting against the dark greens and brown that made up said forest.

The Spectre slowed it's drive, turning when it neared Vien. The Passengers got out quickly, pulling a large sack from the back. The driver slowly walked to the Kaidon, kneeling in sight of the important ruler.

"My Kaidon!" The driver Sangheili spoke up. "We've discovered an intruder while on a hunting expedition, a machine of unknown creation."

"What happened?" Vien examined the strange droid. He had never seen anything like it, except like some nightmarish version of a huragok. It was made of a dark black metal, multiple legs and weapons. Most likely designed to scout.

"It fired on us, so we fired back." The driver chuckled, patting the sizzled remains of the droid. "We were hunting when this machine fired refined plasma, but my shields were more than capable to deal with the surprise. It didn't stand a chance against our rifles."

"Notify the council, this is clearly of foreign design." He observed. "And bring the machine to the humans, they'll know how to crack open anything useful."

"Right away my Kaidon." The much younger pair of Sangheili bowed before returning to their Specter with the probe droid.

Jah 'Zahran stood next to the Kaidon, crossing his arms as the two young Sangheili carried the probe off in the Spectre.

"What do you think uncle? Have the bastard Shyuum and their puppets dared to make a return?"

"Unlikely." Vien paused. "As I said, that was of a foreign design, and the deceivers are decimated, we sought to that personally when we dealt with Mercy and Regret remember? And with Truth's death by the hands of Commander Thel? Not a chance in the after life. Despite what the humans fear, they are of no concern."

"Then what?" Jah questioned again, feeling insecure that an intruder of unknown entity managed to sneak into his world.

Vien didn't answer, instead, he took a moment to look at the night sky, and the stars above. He could only hope that whatever was out there, that they weren't looking for war.

For their sake.

 **Please leave reviews, because guys, I was really happy with the positive reviews from my little timeline alone. Thanks for reading, please, tell me whats right or wrong to you, I want this to be enjoyable for me and you all, and quality feedback is important!**

 **Oh and special thanks to** swordofsangheilios **, Usernamesarebad, and reza0807 for creative assistance!**

 **And on top of that, this is my least favorite chapter that I'm working on** to **be honest. It's just so, dull to me, I guess I had a somewhat difficult time setting up the scenes. But who cares? You're probably not even reading this!**


	3. Chapter 2

Thanks for the nice feedback guys! I'm really happy you guys are full of questions that I'll happily have answered soon. As always keep supplying those reviews, good or bad, I love feedback.

Now onto the story!

Section I: Aggressive Expansion

Chapter 2

1 BBY

Unknown Regions

Imperial II Star Destroyer

Main Bridge

The Imperial Captain rubbed his fingers through his well-groomed hair, quickly returning his officer's hat on his head. His eyes watched a lone asteroid flying aimlessly in the cold space until it was caught by the gravity of the orange-yellow star that glowed with a luminous presence over the small planet that the Imperial fleet orbited.

A dozen Imperial II Star Destroyers, two Imperial I Star Destroyers, and three Interdictor-class cruisers all stood without any sign of movement.

Safely inside the bridge of the leading Star Destroyer, Captain Pallaeon kept careful eyes on everything around him, both inside and out of the ship. Something felt, off, in the bridge. He turned slightly to his left, an aide walking up to one of the communication officers. They talked briefly, the officer pointing at the screen in surprise until both flinched from something on the screen.

That was more than enough for Palleaon to take an interest. He took another look out into space, then turned. A few strides proved enough to cross along the bridge. He calmly stood behind the two, arms behind his back.

"Oh, sir!" The officer hadn't realized he who was standing there. Palleaon nodded his chin forward, gesturing to the still image of green energy surging over the camera lens of the probe droid. Both stood at attention, only to sit back down with Palleaon's second nod.

"Replay the footage."

The officer nodded, typing in a simple command, and said footage was replayed. Palleaon watched silently as a group of undocumented aliens waddled around the probe droid's perimeter, their curiosity was well present.

The probe droid moved about, before stopping to examine another alien, this one was a bird like bipedal walking creature with an alien rifle.

The two engaged briefly, the surprised alien quickly disabled and the probe fired at the possibly hostile targets until it was hit by a wave of green energy, and the footage quickly ended.

"What should we do, sir?"

"Let it be captured, report any new findings to me first and foremost. I must have word with the Admiral." He rubbed under his cap.

"As you wish, Captain."

July 7th, 2532 (UEG Calendar)

High Charity, Covenant Holy City

Ninth Age of Reclamation

High Council Chambers

A hundred thousand probes tore from slipspace and scanned with electronic 'eyes' across the empty void of space. They collected data and flew across the cold vacuum surrounding them. A thousand tears in realspace darted across the area, with the hundreds of carriers and hundreds of more cruisers, all recovering the probes that had quickly analyzed the entirety of the area. A final hole torn open from slipspace, with a massive station who's bulbous exterior seemed to dominate the very heavens themselves.

Hundreds of ships of all classes were scattered around the station. From the common battlecruisers and frigates, to even many of the dreaded supercarriers, the fleet was the most massive Covenant fleet ever witnessed by any being.

Not a single rock larger than even a mere centimeter could enter a ten thousand kilometer wide perimeter without being identified, targeted, and vaporized by one of the millions of weapons that High Charity itself, and its escort fleet, all carried.

Battlecruisers floated, aided by a pair of frigates under it, and three of these trios would stand under a carrier. This formation performed efficiently in all kinds of tasks they needed to perform, such as planetary assault, defense, escort, and even glassing operations. Each battle group, each fleet, worked together and operated in a fashion of independence of other fleets, but could still function together as a unit. New naval doctrines ensured that. With humanity's introduction, the New Covenant had now vastly improved in their Naval organization.

High Charity drifted between the impervious defenses, knowing nothing in any galaxy could match the sheer power of both it and the fleet possessed.

Deep within, the holy city was filled with millions of high ranked members of all the member species. Legions of the greatest Covenant soldiers protected the entirety of the massive city, most of which guarded the high council member's personal quarters, and the great hall of councils.

Supreme Commander Thel 'Vadamee rubbed the underside of his mandible in thought. The holographic details displayed on the massive table of thick nanomalite. Around the large circular base was over a dozen seats, each filled by high ranking officials of each member species. Usually, there were two or more, depending on the species. The humans and Sangheili for example had three elected officials at various given times. But lower species or species that were instead represented by the Sangheili, such as the Lekgolo, were mostly not present. The Jiralhanae, more commonly nicknamed as brutes, had one High Chieftain, and the Kig-yar had a single ambassador from their Empress herself.

Standing by the right of Thel was Admiral Lord Hood, who was the military representative, just like Thel was. To his left was the often angry Chieftain, Khan. The very brute who slayed Tartarus himself and took the very powerful hammer the brute puppet once held.

"We've had reports coming in from at least a dozen systems. Random, outer colonies ranging from agriculture to research in terms of use. The reports are pretty similar, a large object falls onto the planet, releasing this construct." The Admiral gestured the models of the Imperial probe droid. "The machines seem to be programmed in a search and scout function, often getting too close for safety and wind up being destroyed."

A recording of an Unggoy worker singlehandedly disabling one was shown, followed by another probe being cut through by plasma rifles, and another of one being simply smashed by a Brute Captain's gravity hammer. The last said clip made Khan chuckle, a show of pride to the strength of his race.

"We fear, however, that they managed to transmit even the smallest amount of data to whatever pod they came from."

"We have no idea how long they have watched, or more importantly, why." Vien Zahran stated calmly, his fingers clicking together before relaxing his arms.

"Then it is obvious." Imperial Admiral Xytan 'Jar Wattinree sat forward in his polished command chair. "We send a cruiser to their nest, snuff them out and crush whatever is causing this annoyance!" He clenched his fist with but a hint of anger, merely showing off his readiness to achieve dominance.

Many of the races' officials quietly nodded in agreement. Most were thinking to themselves, still in a bit of shock of the reveal.

Hood cleared his throat. "Well, we do have many ships following any pattern we can think of."

Thel nodded, rising from his chair and giving a quick bow. The gold armored elite turned his ceremonial cape around his back.

"If there is nothing more for me to hear, I must leave. Rumors of an infestation in a temple site beckon my fleet."

"You may leave Commander." UEG Governor Nils Thune bowed respectfully.

Thel nodded without another word, leaving the room with a pair of majors that waited for him outside the doors. The three Sangheili matched each other's walk, passing the walls littered with paintings and murals of thousands of victories the Covenant had over the many centuries.

Unknown Regions

Imperial II Star Destroyer, Chimaera

Admiral's quarters

His boots silently pressed against the floor of the hallway. Palleaon smiled slightly to a pair of patrolling stormtroopers, their bulky white armor reminding him of the stories of the clone wars. After all, they were the effective predecessors of the clone troopers from the old republic.

The two troopers remained their stance and kept quiet while passing Palleaon.

Captain Palleaon brushed his mustache with his fingers, not a hair off. He always maintained a formal posture when meeting his superior. Especially the red eyed humanoid sitting at his desk. His expressionless face looking deeply into what he had spent the past half hour reading.

Admiral Thrawn looked up to see Palleaon, casually swiping away the report on the Death Star's completion. In truth he cared little about its construction, to him, it was little more than a large target and waste of resources. But his opinion on the matter held little ground when he was always in the Unknown Regions and nowhere near the galactic center or the Emperor himself.

"Grand Admiral Thrawn, I'm here to report that our probes have found something." Pallaeon straightened his back.

"And you couldn't tell me from the bridge, is something wrong?" Thrawn's deep red eyes seemed to analyze the very soul in Pallaeon.

"I mean to be cautious. I don't trust even half the crew, especially the jumpy ones." He braced himself for anything the Grand Admiral would do.

"You've discovered something." He understood, relaxed and waiting to listen.

"Yes, sir." Palleaon took a step closer. "As of a few hours from now, multiple probe droids you ordered to be sent out are offline. Nearly half, in fact. With only a few being able to provide any footage or readings. I wager that we've stumbled into someone's territory."

"Return to the bridge, send me everything you have." The Admiral ordered without a sign of reaction whatsoever.

After a moment, Palleaon nodded, quietly leaving the room. Only till after the door locked did Grand Admiral Thrawn open a once sealed file in his holotable. In a few moments, a blurry image of a hulking, four mandibled alien appear. It's double bladed plasma sword held still in the air.

Thrawn rubbed his chin, a small sign of curiosity could be clearly seen. His breathing slowed. His red eyes shifted to the much smaller Chiss soldier grabbing at the alien's hand, which wrapped easily around the blue humanoid's neck. His thoughts paced from his youth to the present, and his mind kept going through the possibilities. There was no doubt, the technology was too identical, and the species were the exact ones that killed so many lives all those years ago.

One of his only fears had finally come.

He found them.

Now, he had to see if they would come and find him.

Sorry if this is kinda short for you guys. I'm going to try to make these chapters much longer. Unfortunately, however, school is as busy as always, so don't expect a rapid deployment of chapters. And my dog hasn't been doing too good.

Anyways, I am off!


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